scholarly journals DNA synthesis by Pol η promotes fragile site stability by preventing under-replicated DNA in mitosis

2013 ◽  
Vol 201 (3) ◽  
pp. 395-408 ◽  
Author(s):  
Valérie Bergoglio ◽  
Anne-Sophie Boyer ◽  
Erin Walsh ◽  
Valeria Naim ◽  
Gaëlle Legube ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Fragile Site ◽  
Fragile Sites ◽  
Nuclear Bodies ◽  
Replication Checkpoint ◽  
Genome Damage ◽  
Fork Stalling ◽  
The Stability

Human DNA polymerase η (Pol η) is best known for its role in responding to UV irradiation–induced genome damage. We have recently observed that Pol η is also required for the stability of common fragile sites (CFSs), whose rearrangements are considered a driving force of oncogenesis. Here, we explored the molecular mechanisms underlying this newly identified role. We demonstrated that Pol η accumulated at CFSs upon partial replication stress and could efficiently replicate non-B DNA sequences within CFSs. Pol η deficiency led to persistence of checkpoint-blind under-replicated CFS regions in mitosis, detectable as FANCD2-associated chromosomal sites that were transmitted to daughter cells in 53BP1-shielded nuclear bodies. Expression of a catalytically inactive mutant of Pol η increased replication fork stalling and activated the replication checkpoint. These data are consistent with the requirement of Pol η–dependent DNA synthesis during S phase at replication forks stalled in CFS regions to suppress CFS instability by preventing checkpoint-blind under-replicated DNA in mitosis.

scholarly journals Werner syndrome helicase activity is essential in maintaining fragile site stability

2008 ◽  
Vol 180 (2) ◽  
pp. 305-314 ◽  
Author(s):  
Livia Maria Pirzio ◽  
Pietro Pichierri ◽  
Margherita Bignami ◽  
Annapaola Franchitto
Keyword(s):  
Werner Syndrome ◽  
Fragile Site ◽  
Chromosome Breakage ◽  
Fragile Sites ◽  
Helicase Activity ◽  
Dna Helicases ◽  
Replication Checkpoint ◽  
Replicative Stress ◽  
Fork Stalling ◽  
The Stability

WRN is a member of the RecQ family of DNA helicases implicated in the resolution of DNA structures leading to the stall of replication forks. Fragile sites have been proposed to be DNA regions particularly sensitive to replicative stress. Here, we establish that WRN is a key regulator of fragile site stability. We demonstrate that in response to mild doses of aphidicolin, WRN is efficiently relocalized in nuclear foci in replicating cells and that WRN deficiency is associated with accumulation of gaps and breaks at common fragile sites even under unperturbed conditions. By expressing WRN isoforms impaired in either helicase or exonuclease activity in defective cells, we identified WRN helicase activity as the function required for maintaining the stability of fragile sites. Finally, we find that WRN stabilizes fragile sites acting in a common pathway with the ataxia telangiectasia and Rad3 related replication checkpoint. These findings provide the first evidence of a crucial role for a helicase in protecting cells against chromosome breakage at normally occurring replication fork stalling sites.

scholarly journals Making of fusion genes in cancer: An in-silico study of mechanism of chromosomal translocations

2018 ◽  
Author(s):  
Kiran Lalwani ◽  
Shivani Sheth ◽  
Inayatullah Sheikh ◽  
Afzal Ansari ◽  
Fulesh Kunwar ◽  
...  
Keyword(s):  
Dna Sequences ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Fusion Gene ◽  
Genetic Material ◽  
Chromosomal Translocations ◽  
In Silico Study ◽  
Clinical Consequences ◽  
The Stability ◽  
Genomic Regions

Chromosomal translocations involve exchange of genetic material between non- homologous chromosomes leading to the formation of a fusion gene with altered function. The clinical consequences of non-random and recurrent chromosomal translocations have been so well understood in carcinogenesis that they serve as diagnostic and prognostic markers and also help in therapy decisions, mainly in leukemia and lymphoma. However, the molecular mechanisms underlying these recurrent genetic exchanges are yet to be understood. Various approaches employed include the extent of the vicinity of the partner chromosomes in the nucleus, DNA sequences at the breakpoints, etc. The present study addresses the stability of DNA sequences at the breakpoint regions using in-silico approach in terms of physicochemical properties such as; AT%, flexibility, melting temperature, enthalpy, entropy, stacking energy and free energy. Changes in these properties may lead to instability of DNA which could affect gene expression in particular and genome organization in general. Our study indicates that the fusion sequences are comparatively more unstable and hence, more prone to breakage. Current study along with others could lead to developing a model for predicting breakage prone genomic regions using this novel in-silico approach.

scholarly journals BRCA1 Is Required for Common-Fragile-Site Stability via Its G2/M Checkpoint Function

2004 ◽  
Vol 24 (15) ◽  
pp. 6701-6709 ◽  
Author(s):  
Martin F. Arlt ◽  
Bo Xu ◽  
Sandra G. Durkin ◽  
Anne M. Casper ◽  
Michael B. Kastan ◽  
...  
Keyword(s):  
Rna Interference ◽  
Tumor Suppressor ◽  
Dna Synthesis ◽  
Cancer Cells ◽  
Tumor Suppressor Genes ◽  
Fragile Site ◽  
Fragile Sites ◽  
Common Fragile Site ◽  
Interacting Proteins ◽  
Checkpoint Pathway

ABSTRACT Common fragile sites are loci that form chromosome gaps or breaks when DNA synthesis is partially inhibited. Fragile sites are prone to deletions, translocations, and other rearrangements that can cause the inactivation of associated tumor suppressor genes in cancer cells. It was previously shown that ATR is critical to fragile-site stability and that ATR-deficient cells have greatly elevated fragile-site expression (A. M. Casper, P. Nghiem, M. F. Arlt, and T. W. Glover, Cell 111:779-789, 2002). Here we demonstrate that mouse and human cells deficient for BRCA1, due to mutation or knockdown by RNA interference, also have elevated fragile-site expression. We further show that BRCA1 functions in the induction of the G2/M checkpoint after aphidicolin-induced replication stalling and that this checkpoint function is involved in fragile-site stability. These data indicate that BRCA1 is important in fragile-site stability and that fragile sites are recognized by the G2/M checkpoint pathway, in which BRCA1 plays a key role. Furthermore, they suggest that mutations in BRCA1 or interacting proteins could lead to rearrangements at fragile sites in cancer cells.

scholarly journals And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break

2017 ◽  
Vol 372 (1731) ◽  
pp. 20160291 ◽  
Author(s):  
P. Christopher Caridi ◽  
Laetitia Delabaere ◽  
Grzegorz Zapotoczny ◽  
Irene Chiolo
Keyword(s):  
Dna Sequences ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Nuclear Periphery ◽  
Strand Break ◽  
Double Strand Break ◽  
Chromatin Dynamics ◽  
Recombination Repair ◽  
The Stability

Heterochromatin is mostly composed of repeated DNA sequences prone to aberrant recombination. How cells maintain the stability of these sequences during double-strand break (DSB) repair has been a long-standing mystery. Studies in Drosophila cells revealed that faithful homologous recombination repair of heterochromatic DSBs relies on the striking relocalization of repair sites to the nuclear periphery before Rad51 recruitment and repair progression. Here, we summarize our current understanding of this response, including the molecular mechanisms involved, and conserved pathways in mammalian cells. We will highlight important similarities with pathways identified in budding yeast for repair of other types of repeated sequences, including rDNA and short telomeres. We will also discuss the emerging role of chromatin composition and regulation in heterochromatin repair progression. Together, these discoveries challenged previous assumptions that repair sites are substantially static in multicellular eukaryotes, that heterochromatin is largely inert in the presence of DSBs, and that silencing and compaction in this domain are obstacles to repair. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.

scholarly journals Reduced Levels of DNA Polymerase δ Induce Chromosome Fragile Site Instability in Yeast

2008 ◽  
Vol 28 (17) ◽  
pp. 5359-5368 ◽  
Author(s):  
Francene J. Lemoine ◽  
Natasha P. Degtyareva ◽  
Robert J. Kokoska ◽  
Thomas D. Petes
Keyword(s):  
Dna Polymerase ◽  
Cancer Biology ◽  
Molecular Mechanisms ◽  
Fragile Site ◽  
Fragile Sites ◽  
Dna Lesions ◽  
Catalytic Subunit ◽  
Dna Breaks ◽  
Dna Polymerase Δ ◽  
Double Strand Dna Breaks

ABSTRACT Specific regions of genomes (fragile sites) are hot spots for the chromosome rearrangements that are associated with many types of cancer cells. Understanding the molecular mechanisms regulating the stability of chromosome fragile sites, therefore, has important implications in cancer biology. We previously identified two chromosome fragile sites in Saccharomyces cerevisiae that were induced in response to the reduced expression of Pol1p, the catalytic subunit of DNA polymerase α. In the study presented here, we show that reduced levels of Pol3p, the catalytic subunit of DNA polymerase δ, induce instability at these same sites and lead to the generation of a variety of chromosomal aberrations. These findings demonstrate that a change in the stoichiometry of replicative DNA polymerases results in recombinogenic DNA lesions, presumably double-strand DNA breaks.

Fragile Genes That Are Frequently Altered in Cancer: Players Not Passengers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 208-216 ◽  
Author(s):  
Jenna R. Karras ◽  
Morgan S. Schrock ◽  
Bahadir Batar ◽  
Kay Huebner
Keyword(s):  
Genome Instability ◽  
Fragile Site ◽  
Replication Stress ◽  
Fragile Sites ◽  
Gap Formation ◽  
A Genome ◽  
Protein Functions ◽  
Fhit Protein ◽  
The Stability ◽  
Selection Of

FHIT, located at FRA3B, is one of the most commonly deleted genes in human cancers, and loss of FHIT protein is one of the earliest events in cancer initiation. However, location of FHIT at a chromosomal fragile site, a locus prone to breakage and gap formation under even mild replication stress, has encouraged claims that FHIT loss is a passenger event in cancers. We summarize accumulated evidence that FHIT protein functions as a genome “caretaker” required to protect the stability of genomes of normal cells of most tissues from agents causing intrinsic and extrinsic DNA damage. FHIT loss leads to intracellular replication stress and subsequent genome instability, which provides an opportunistic mutational landscape in preneoplasias for selection of a variety of other cancer-driving mutations. We also review evidence showing that FHIT loss leads to enhanced activation of other common fragile sites, including the FRA16D/WWOX locus, and creates optimal single-stranded DNA substrates for the hypermutator enzyme, APOBEC3B.

scholarly journals Making of fusion genes in cancer: An in-silico study of mechanism of chromosomal translocations

2018 ◽  
Author(s):  
Kiran Lalwani ◽  
Shivani Sheth ◽  
Inayatullah Sheikh ◽  
Afzal Ansari ◽  
Fulesh Kunwar ◽  
...  
Keyword(s):  
Dna Sequences ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Fusion Gene ◽  
Genetic Material ◽  
Chromosomal Translocations ◽  
In Silico Study ◽  
Clinical Consequences ◽  
The Stability ◽  
Genomic Regions

Chromosomal translocations involve exchange of genetic material between non- homologous chromosomes leading to the formation of a fusion gene with altered function. The clinical consequences of non-random and recurrent chromosomal translocations have been so well understood in carcinogenesis that they serve as diagnostic and prognostic markers and also help in therapy decisions, mainly in leukemia and lymphoma. However, the molecular mechanisms underlying these recurrent genetic exchanges are yet to be understood. Various approaches employed include the extent of the vicinity of the partner chromosomes in the nucleus, DNA sequences at the breakpoints, etc. The present study addresses the stability of DNA sequences at the breakpoint regions using in-silico approach in terms of physicochemical properties such as; AT%, flexibility, melting temperature, enthalpy, entropy, stacking energy and free energy. Changes in these properties may lead to instability of DNA which could affect gene expression in particular and genome organization in general. Our study indicates that the fusion sequences are comparatively more unstable and hence, more prone to breakage. Current study along with others could lead to developing a model for predicting breakage prone genomic regions using this novel in-silico approach.

scholarly journals AT-dinucleotide rich sequences drive fragile site formation

2019 ◽  
Vol 47 (18) ◽  
pp. 9685-9695 ◽  
Author(s):  
Michal Irony-Tur Sinai ◽  
Anita Salamon ◽  
Noemie Stanleigh ◽  
Tchelet Goldberg ◽  
Aryeh Weiss ◽  
...  
Keyword(s):  
Dna Replication ◽  
Human Genome ◽  
Dna Sequences ◽  
Fragile Site ◽  
Integration Site ◽  
Replication Stress ◽  
Secondary Structures ◽  
Fragile Sites ◽  
Stable Region ◽  
Site Formation

Abstract Common fragile sites (CFSs) are genomic regions prone to breakage under replication stress conditions recurrently rearranged in cancer. Many CFSs are enriched with AT-dinucleotide rich sequences (AT-DRSs) which have the potential to form stable secondary structures upon unwinding the double helix during DNA replication. These stable structures can potentially perturb DNA replication progression, leading to genomic instability. Using site-specific targeting system, we show that targeted integration of a 3.4 kb AT-DRS derived from the human CFS FRA16C into a chromosomally stable region within the human genome is able to drive fragile site formation under conditions of replication stress. Analysis of >1300 X chromosomes integrated with the 3.4 kb AT-DRS revealed recurrent gaps and breaks at the integration site. DNA sequences derived from the integrated AT-DRS showed in vitro a significantly increased tendency to fold into branched secondary structures, supporting the predicted mechanism of instability. Our findings clearly indicate that intrinsic DNA features, such as complexed repeated sequence motifs, predispose the human genome to chromosomal instability.

scholarly journals A catalytic-independent function of human DNA polymerase Kappa controls the pool of the Checkpoint Kinase 1

2021 ◽  
Author(s):  
Marina Dall’Osto ◽  
Laura Pierini ◽  
Nicolas Valery ◽  
Jean-Sébastien Hoffmann ◽  
Marie-jeanne Pillaire
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Genome Stability ◽  
Replication Process ◽  
Replication Checkpoint ◽  
Protein Pool ◽  
Synthesis Activity ◽  
The Stability ◽  
Y Family ◽  
Major Mediator

ABSTRACTDNA polymerase kappa (Pol κ) has been well documented thus far for its specialized DNA synthesis activity during translesion replication, progression of replication forks through regions difficult to replicate and replication checkpoint at stalled forks.Here we unveiled an unexpected role for Pol κ in controlling the stability and abundance of Chk1, the major mediator of the replication checkpoint. We found that loss of Pol κ decreased the Chk1 protein level in the nucleus of four human cell lines. Pol κ and not the other Y‐family polymerase members is required to maintain the Chk1 protein pool all along the cell cycle. We showed that Pol κ depletion affected the protein stability of Chk1 and protected it from proteasome degradation and the replication recovery defects observed in Pol κ-depleted cells could be overcome by the re-expression of Chk1. Importantly, this new function of Pol κ does not require its catalytic activity, revealing that in addition to its known roles in the replication process, Pol κ can contribute to the maintenance of genome stability independently of its DNA synthesis activity.

scholarly journals Minichromosome Maintenance Proteins Interact with Checkpoint and Recombination Proteins To Promote S-Phase Genome Stability

2008 ◽  
Vol 28 (5) ◽  
pp. 1724-1738 ◽  
Author(s):  
Julie M. Bailis ◽  
Douglas D. Luche ◽  
Tony Hunter ◽  
Susan L. Forsburg
Keyword(s):  
Dna Synthesis ◽  
Replication Fork ◽  
Genome Stability ◽  
S Phase ◽  
Minichromosome Maintenance ◽  
Replication Checkpoint ◽  
Recombination Proteins ◽  
Mcm Complex ◽  
Mcm Proteins ◽  
The Stability

ABSTRACT The minichromosome maintenance (MCM) complex plays essential, conserved roles throughout DNA synthesis: first, as a component of the prereplication complex at origins and, then, as a helicase associated with replication forks. Here we use fission yeast (Schizosaccharomyces pombe) as a model to demonstrate a role for the MCM complex in protecting replication fork structure and promoting recovery from replication arrest. Loss of MCM function generates lethal double-strand breaks at sites of DNA synthesis during replication elongation, suggesting replication fork collapse. MCM function also maintains the stability of forks stalled by hydroxyurea that activate the replication checkpoint. In cells where the checkpoint is activated, Mcm4 binds the Cds1 kinase and undergoes Cds1-dependent phosphorylation. MCM proteins also interact with proteins involved in homologous recombination, which promotes recovery from arrest by ensuring normal mitosis. We suggest that the MCM complex links replication fork stabilization with checkpoint arrest and recovery through direct interactions with checkpoint and recombination proteins and that this role in S-phase genome stability is conserved from yeast to human cells.

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